MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating N in Genetic Monitoring Programs.

We introduce a new software program, MaxTemp, that increases precision of the temporal method for estimating effective population size (N) in genetic monitoring programs, which are increasingly used to systematically track changes in global biodiversity. Scientists and managers are typically most interested in N for individual generations, either to match with single-generation estimates of census size (N) or to evaluate consequences of specific management actions or environmental events. Systematically sampling every generation produces a time series of single-generation estimates of temporal F ( , which can then be used to estimate N; however, these estimates have relatively low precision because each reflects just a single episode of genetic drift.

My Ancestors Were One-Celled Organisms.

This first-person essay explores wonder in the medical encounter from a patient's point of view, considering times when medical technology has given the author insight into her body and the wonder that has been evoked by these experiences. Two medical encounters are detailed: one in which post-polio vocal cord weakness was explored using a miniature camera, which evoked a sense of wonder at the process of evolution; and the second in which an MRI of the author's skull became a memento mori. The author reflects on the long processes of genetic mutation from single-celled organism to human being, and on the devolution after death to food for bacteria and insects.

Salivary Gland Volume Predicts Malnutrition in Irradiated Head and Neck Cancer Patients: A Prospective Analysis.

Background/aim: Xerostomia following (chemo-) radiotherapy (CRT) is common in head and neck (HNC) patients. This prospective study focused on investigating the link between salivary gland function and the onset of malnutrition in HNC patients.

Patients And Methods: Between 2018 and 2020, 61 HNC patients scheduled for curative CRT were prospectively recruited.

nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer.

The pleiotropic roles of nSMase2-generated ceramide include regulation of intracellular ceramide signaling and exosome biogenesis. We investigated the effects of eliminating nSMase2 on early and advanced PDA, including its influence on the microenvironment. Employing the KPC mouse model of pancreatic cancer, we demonstrate that pancreatic epithelial nSMase2 ablation reduces neoplasia and promotes a PDA subtype switch from aggressive basal-like to classical.

Lessons learnt on infectious bronchitis virus lineage GI-23.

Infectious bronchitis virus (IBV) is the first coronavirus discovered in the world in the early 1930s and despite decades of extensive immunoprophylaxis efforts, it remains a major health concern to poultry producers worldwide. Rapid evolution due to large poultry population sizes coupled with high mutation and recombination events and the reliance of the antiviral immune response on specific antibodies against the epitopes of the S1 glycoprotein, render the control of IBV extremely challenging. The numerous and rapidly evolving genetic and antigenic IBV types are currently classified based on the whole S1 gene sequence, into 36 lineages clustered in eight genotypes.

Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery.

A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt.

Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches.

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey.

Loss of plasticity in maturation timing after ten years of captive spawning in a delta smelt conservation hatchery.

Adaptation to captivity in spawning programs can lead to unintentional consequences, such as domestication that results in reduced fitness in the wild. The timing of sexual maturation has been shown to be a trait under domestication selection in fish hatcheries, which affects a fish's access to mating opportunities and aligning their offspring's development with favorable environmental conditions. Earlier maturing fish may be favored in hatchery settings where managers provide artificially optimal growing conditions, but early maturation may reduce fitness in the wild if, for example, there is a mismatch between timing of reproduction and availability of resources that support recruitment.

Immunization and Host Responses to , a Live Hatchery Vaccine against Infectious Bursal Disease.

is an attenuated infectious bursal disease virus vaccine. Previously, we observed a temporal delay of vaccine virus replication in the bursae of chicks due to maternally derived antibodies (MDAs). The mechanism that allowed its survival despite MDA neutralization remained unclear.

Irradiation dose to the swallowing apparatus impacts nutritional status in head and neck cancer patients-results from the prospective randomized HEADNUT trial.

Purpose: To investigate the influence of radiation dose to the swallowing muscles on the nutritional status in patients with head and neck cancer undergoing primary or adjuvant (chemo)radiotherapy (C)RT.

Methods: Between 2018 and 2020, 61 patients were prospectively randomized into the so-called HEADNUT trial (head and neck cancer patients undergoing nutritional intervention). Follow-up was continued until 2022.

Development of toxin-antitoxin self-destructive bacteria, aimed for salmonella vaccination.

The most common source of foodborne Salmonella infection in humans is poultry eggs and meat, such that prevention of human infection is mostly achieved by vaccination of farm animals. While inactivated and attenuated vaccines are available, both present drawbacks. This study aimed to develop a novel vaccination strategy, which combines the effectiveness of live-attenuated and safety of inactivated vaccines by construction of inducible self-destructing bacteria utilizing toxin-antitoxin (TA) systems.

Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock.

A defining property of circadian clocks is temperature compensation, characterized by the resilience of their near 24-hour free-running periods against changes in environmental temperature within the physiological range. While temperature compensation is evolutionary conserved across different taxa of life and has been studied within many model organisms, its molecular underpinnings remain elusive. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions.

Captive-reared Delta Smelt (Hypomesus transpacificus) exhibit high survival in natural conditions using in situ enclosures.

Conservation of endangered fishes commonly includes captive breeding, applied research, and management. Since 1996, a captive breeding program has existed for the federally threatened and California endangered Delta Smelt Hypomesus transpacificus, an osmerid fish endemic to the upper San Francisco Estuary. Although this program serves as a captive refuge population, with experimental releases being initiated to supplement the wild population, it was uncertain how individuals would survive, feed, and maintain condition outside hatchery conditions.

Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River.

Rainbow Trout, Oncorhynchus mykiss, exhibit high levels of phenotypic diversity leading to the recognition of numerous subspecies. A major distinction among Rainbow Trout subspecies exists between Coastal Rainbow Trout (O. m.

FPIES: Data for Germany in international comparison.

Food protein-induced enterocolitis syndrome (FPIES) is a rare, non-IgE-mediated food allergy. The triggering foods differ significantly from the typical triggers of an IgE-mediated food allergy. Until recently, there were no data on triggers of FPIES in Germany.

A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli.

We present the novel reference genome of the Versatile Fairy Shrimp, Branchinecta lindahli. The Versatile Fairy Shrimp is a freshwater anostracan crustacean found across the western United States from Iowa to Oregon and from Alberta to Baja California. It is an ephemeral pool specialist, living in prairie potholes, irrigation ditches, tire treads, vernal pools, and other temporary freshwater wetlands.

A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi.

We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California's freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries.

The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi.

In this paper, we report on the scaffold-level assembled genome for the federally endangered, California endemic crustacean Lepidurus packardi (the Vernal Pool Tadpole Shrimp). L. packardi is a key food source for other conserved California species including the California Tiger Salamander Ambystoma californiense.

Impact of dosimetric factors on long-term percutaneous enteral gastrostomy (PEG) tube dependence in head and neck cancer patients after (chemo)radiotherapy-results from a prospective randomized trial.

Purpose/objective: To analyze dose-volume histogram (DVH)-derived data on the exposure of organs at risk with impact on long-term percutaneous enteral gastrostomy (PEG) tube dependence in head and neck cancer patients at 6 and 12 months after definitive or adjuvant (chemo)radiotherapy.

Materials And Methods: Sixty-one patients were prospectively treated with (chemo)radiotherapy. Prophylactic or reactive gastrostomy tube placement was performed in 41 (67.

Polygenic discrimination of migratory phenotypes in an estuarine forage fish.

Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt.

In Vitro Assays for Measuring Intercellular Coupling Among Peripheral Circadian Oscillators.

Circadian clocks can be found in nearly all eukaryotic organisms, as well as certain bacterial strains, including commensal microbiota. Exploring intercellular coupling among cell-autonomous circadian oscillators is crucial for understanding how cellular ensembles generate and sustain coherent circadian rhythms on the tissue level, and thus, rhythmic organ functions. Here we describe a protocol for studying intercellular coupling among peripheral circadian oscillators using three-dimensional spheroid cultures in order to measure coupling strength within peripheral clock networks.